Realized in my tooling around I had flipped T1 and hippoSf in my command. Here is how the adjustment needs to be made for:
quantifyHAsubregions.sh hippoSf <T1>-<analysisID> <output_file> <OPTIONAL_SUBJECTS_DIR>

 leftVolFile="$resultsDirectory/$subjectName/mri/lh.${prefix}Volumes-${suffix}.v20.txt"
 rightVolFile="$resultsDirectory/$subjectName/mri/rh.${prefix}Volumes-${suffix}.v20.txt"

On Tue, Sep 19, 2017 at 9:23 AM, Josh Gray <jgray7700@gmail.com> wrote:
Hello,

I found a small bug in recent dev version bin quantifyHAsubregions.sh:
 leftVolFile="$resultsDirectory/$subjectName/mri/lh.${suffix}Volumes-${suffix}.v20.txt"
 rightVolFile="$resultsDirectory/$subjectName/mri/rh.${suffix}Volumes-${suffix}.v20.txt"


Should say
 leftVolFile="$resultsDirectory/$subjectName/mri/lh.${suffix}Volumes-${prefix}.v20.txt"
 rightVolFile="$resultsDirectory/$subjectName/mri/rh.${suffix}Volumes-${prefix}.v20.txt"


because as specified "T1" is the ${prefix} which is how the subfields file names end. Obviously, can flip suffix and prefix throughout so it is more intuitive. Seems to work fine after this adjustment.

Josh
--
Joshua C. Gray, PhD
Psychology Instructor
Center for Deployment Psychology



--
Joshua C. Gray, PhD
Psychology Instructor
Center for Deployment Psychology